Merge branch 'main' into niche_definitions

Author: timtreis

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.5.0
+current_version = 1.6.0
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)

.github/workflows/test.yml

@@ -23,10 +23,11 @@ jobs:
                 python: [3.9, "3.10", "3.11"]
                 os: [ubuntu-latest]
                 include:
-                    - python: 3.9
-                      os: macos-latest
-                    - python: "3.10"
+                    - python: "3.12"
                       os: macos-latest
+                      pip-flags: "--pre"
+                      name: "Python 3.12 (pre-release)"
+
         env:
             OS: ${{ matrix.os }}
             PYTHON: ${{ matrix.python }}

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.10.0
+      rev: v1.11.0
       hooks:
           - id: mypy
             additional_dependencies: [numpy, pandas, types-requests]
@@ -46,7 +46,7 @@ repos:
             name: Check executable files use .sh extension
             types: [shell, executable]
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.4.5
+      rev: v0.5.4
       hooks:
           - id: ruff
             types_or: [python, pyi, jupyter]

docs/api.rst

@@ -14,6 +14,7 @@ Graph
     :toctree: api
 
     gr.spatial_neighbors
+    gr.mask_graph
     gr.nhood_enrichment
     gr.co_occurrence
     gr.centrality_scores

docs/conf.py

@@ -94,6 +94,7 @@
     omnipath=("https://omnipath.readthedocs.io/en/latest", None),
     napari=("https://napari.org/", None),
     spatialdata=("https://spatialdata.scverse.org/en/latest", None),
+    shapely=("https://shapely.readthedocs.io/en/stable", None),
 )
 
 # Add any paths that contain templates here, relative to this directory.

docs/release/notes-1.6.0.rst

@@ -0,0 +1,11 @@
+Squidpy 1.6.0 (2024-07-23)
+==========================
+
+Features
+--------
+
+- Now :func:`squidpy.gr.spatial_graph` can also be used on :class:`spatialdata.SpatialData` objects.
+
+- Add :func:`squidpy.gr.mask_graph` to mask a spatial graph based on :class:`shapely.Polygon` or :class:`shapely.MultiPolygon`
+  `@giovp <https://github.com/giovp>`__
+  `#842 <https://github.com/scverse/squidpy/pull/842>`__

pyproject.toml

@@ -72,7 +72,7 @@ dependencies = [
    "validators>=0.18.2",
    "xarray>=0.16.1",
    "zarr>=2.6.1",
-   "spatialdata",
+   "spatialdata>=0.2.0",
 ]
 
 [project.optional-dependencies]

src/squidpy/gr/__init__.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from squidpy.gr._build import spatial_neighbors
+from squidpy.gr._build import mask_graph, spatial_neighbors
 from squidpy.gr._ligrec import ligrec
 from squidpy.gr._nhood import centrality_scores, interaction_matrix, nhood_enrichment
 from squidpy.gr._niche import calculate_niche